Publications

Lerman L, Bontempi G, Markowitch O. The bias-variance decomposition in profiled attacks. Journal of Cryptographic Engineering [Internet]. 2015:1-13.
Jansen M. Generalized Cross Validation in variable selection with and without shrinkage. Journal of Statistical Planning and Inference [Internet]. 2015:90-104.
Claeskens G, Jansen M. International Encyclopedia of the Social & Behavioral Sciences. In: D. Wright J Vol. 15. 2nd ed. ; 2015. p. 647-652.
Lerman L, Bontempi G, Markowitch O. A machine learning approach against a masked AES – Reaching the limit of side-channel attacks with a learning model. J. Cryptographic Engineering [Internet]. 2015:123–139.
Verstraeten N, Knapen W J, Kint C I, Liebens V R, Van den Bergh B, Dewachter L, Fu Q, David C C, Fierro C, Marchal K, et al. Membrane depolarization-triggered responsive diversification to antibiotic tolerance. Molecular Cell [Internet]. 2015:To Appear.
Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DMA, Grossman P, et al. PharmacoGx: An R package for analysis of large pharmacogenomic datasets. Bioinformatics [Internet]. 2015.
Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot TS, Malta TM, Pagnotta SM, Castiglioni I, et al. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Research [Internet]. 2015.
Lerman L, Poussier R, Bontempi G, Markowitch O, Standaert F{-}X. Template Attacks vs. Machine Learning Revisited (and the Curse of Dimensionality in Side-Channel Analysis).
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B. Using shRNA experiments to validate gene regulatory networks. Genomics Data [Internet]. 2015:-.
Ampe EM, Raymaekers D, Hestir EL, Jansen M, Knaeps E, Batelaan O. A wavelet enhanced semi-analytical inversion model for water quality retrieval from high spectral resolution data for complex waters. IEEE Transactions on Geoscience and Remote Sensing [Internet]. 2015:869-882.

Carcillo F, Lima-Mendez G, Faust K, Raes J, Bontempi G. Abundance predictions of operational taxonomic units in ocean samples. [Internet]. 2014.
Cuéllar MP, Le Borgne Y, Galiano-Castillo N, Arroyo M, Pegalajar MC, Martin-Bautista MJ, Bontempi G. An approach for automatic evaluation of diagnosis exercises inphysical therapy using depth sensors.
Trépo E, Nahon P, Bontempi G, Valenti L, Falleti E, Nischalke H-D, Hamza S, Corradini SG, Burza MA, Guyot E, et al. Association between the PNPLA3 (rs738409 C> G) variant and hepatocellular carcinoma: Evidence from a meta-analysis of individual participant data. Hepatology. 2014:2170–2177.
Han TA, Pereira ML, Lenaerts T. Avoiding or restricting defectors in public goods games?. Journal of The Royal Society Interface [Internet]. 2014:20141203.
Ben Taieb S, Hyndman R. Boosting multi-step autoregressive forecasts.

Ghaddar K, Krammer EM, Mihajlovic N, Brohee S, Andre B, Prevost M. Converting the yeast arginine can1 permease to a lysine permease}. J. Biol. Chem. 2014:7232–7246.
Raimondi D, Orlando G, Vranken WF. Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements.Bioinformatics (Oxford, England) [Internet]. 2014:1–7.
Milenkovic D, Vanden Berghe W, Boby C, Leroux C, Declerck K, Szarc vel Szic K, Heyninck K, Laukens K, Bizet M, Defrance M, et al. Dietary flavanols modulate the transcription of genes associated with cardiovascular pathology without changes in their DNA methylation state}. PLoS ONE. 2014:e95527.
Reggiani C, Smits G, Vilain C, Bontempi G. Distinguish between pathogenic and bening cnv in rare disease: a feature selection approach.
Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF. The DynaMine webserver: predicting protein dynamics from sequence. Nucleic Acids Research [Internet]. 2014.
Han TA, Pereira LM, Santos FC, Lenaerts T. Evolution of Pairwise Commitment and Cooperation.
Leon O, Cuéllar MP, Delgado M, Le Borgne Y, G. B. Human Activity Recognition Framework in monitored environments.
Skwark MJ, Raimondi D, Michel M, Elofsson A. Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns. PLoS computational biology [Internet]. 2014:e1003889.
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Haibe-Kains B, Quackenbush J. Inference and validation of predictive gene networks from biomedical literature and gene expression data. Genomics [Internet]. 2014:-.
Jansen M. Information criteria for variable selection under sparsity. {B}iometrika. 2014:37-55.
Dal Pozzolo A, Caelen O, Borgne Y-AL, Waterschoot S, Bontempi G. Learned lessons in credit card fraud detection from a practitioner perspective. Expert Systems with Applications. 2014.
Han TA, Pereira LM, Lenaerts T, Santos FC. Learning to recognize intentions resolves cooperation dilemmas.
Lerman L, Medeiros SF, Bontempi G, Markowitch O. A Machine Learning Approach Against a Masked AES. In: Francillon A, Rohatgi P Smart Card Research and Advanced Applications. Vol. 8419. Smart Card Research and Advanced Applications. ; 2014. p. 61–75.
Lerman L, Bontempi G, Markowitch O. A machine learning approach against a masked AES. Journal of Cryptographic Engineering. 2014:1-17.
Ben Taieb S. Machine learning strategies for multi-step-ahead time series forecasting.
Reggiani C, Borgne Y-AL, Dal Pozzolo A, Olsen C, Bontempi G. Minimum Redundancy Maximum Relevance: MapReduce implementation using Apache Hadoop.
Govorun M, Guy Latouche. Modeling the effect of health: Phase-type approach. Eur. Actuar. J. 2014:197–218.
Bontempi G. A Monte Carlo strategy for structured multiple-step-ahead time series prediction.
Jansen M. Multiscale local polynomial models for estimation and testing. In: Akritas M, Lahiri S N, Politis D Topics in NonParametric Statistics. Vol. 74. Topics in NonParametric Statistics. ; 2014. p. 155-166.
Hautphenne S, Guy Latouche, Nguyen GT. On the nature of Phase-type Poisson distributions. Annals of Actuarial Science. 2014:79–98.
Jansen M. Nonseparable Laplacian Pyramids with Multiscale Local Polynomials for Scattered Data. In: Mustra M, Tralić D, Grgić M, Zovko-Cihlar B Proceedings IWSSIP, 21st International Conference on Systems, Signals and Image Processing. Proceedings IWSSIP, 21st International Conference on Systems, Signals and Image Processing. ; 2014. p. 115-118.
Lopes M, Bontempi G. On the Null Distribution of the Precision and Recall Curve. In: Machine Learning and Knowledge Discovery in Databases. Vol. 8725. Machine Learning and Knowledge Discovery in Databases. ; 2014. p. 322-337.
Iolis B, Bontempi G. Optimizing Component Combination in a Multi-Indexing Paragraph Retrieval System.

Lerman L, Bontempi G, Markowitch O. Power analysis attack: an approach based on machine learning. International Journal of Applied Cryptography. 2014:97-115.
Elisa C, Teso S, Ammendola S, Lenaerts T, Passerini A. Predicting virus mutations through statistical relational learning. BMC bioinformatics [Internet]. 2014:309.
Cuéllar MP, Le Borgne Y, Galiano-Castillo N, Arroyo M, Pegalajar MC, Martin-Bautista MJ, Bontempi G. PReSenS: Towards Smart Rehabilitation with Proactive Sensing for Remote and Automatic Medical Evaluation.
Guy Latouche, Miyazawa M. Product-form characterization for a two-dimensional reflecting random walk. Queueing Systems. 2014:373–391.
Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains B. Relevance of different prior knowledge sources for inferring gene interaction networks. Frontiers in Genetics [Internet]. 2014.
Boumahdi S, Driessens G, Lapouge G, Rorive S, Nassar D, Le Mercier M, Delatte B, Caauwe A, Lenglez S, Nkusi E, et al. SOX2 controls tumour initiation and cancer stem-cell functions in squamous-cell carcinoma}. Nature. 2014:246–250.
Lopes M, Kutlu B, Miani M, Bang-Berthelsen CH, Størling J, Pociot F, Goodman N, Hood L, Welsh N, Bontempi G, et al. Temporal profiling of cytokine-induced genes in pancreatic Beta-cells by meta-analysis and network inference. Genomics. 2014.
Dal Pozzolo A, Johnson R, Caelen O, Waterschoot S, Chawla NV, Bontempi G. Using HDDT to avoid instances propagation in unbalanced and evolving data streams.
Ampe EM, Hestir EL, Bresciani M, Salvadore E, Brando VE, Dekker A, Malthus TJ, Jansen M, Triest L, Batelaan O, et al. A wavelet approach for estimating chlorophyll-a from inland waters. IEEE Geoscience and Remote Sensing Letters. 2014:89-93.

Rubio L, Huculeci R, Buts L, Vanwetswinkel S, Lenaerts T, van Nuland NAJ. (1)H, (13)C, and (15)N backbone and side-chain chemical shift assignments of the free and bound forms of the human PTPN11 second SH2 domain. Advances in hematology [Internet]. 2013.
Trépo E, Nahon P, Bontempi G, Valenti L, Falleti E, Nischalke HD, Hamza S, Corradini SG, Burza MA, Guyot E, et al. Association between the PNPLA3 (rs738409 C> G) variant and hepatocellular carcinoma: evidence from a meta-analysis of individual participant data. Hepatology. 2013.
Papillon-Cavanagh S, De Jay N, Hachem N, Olsen C, Bontempi G, Aerts H, Quackenbush J, Haibe-Kains B. Comparison and Validation of Genomic Predictors for Anticancer Drug Sensitivity. Journal of the American Medical Informatics Association. 2013.
Dedeurwaerder S, Defrance M, Bizet M, Calonne E, Bontempi G, Fuks F. A comprehensive overview of Infinium HumanMethylation450 data processing. Briefings in bioinformatics. 2013:bbt054.
Han TA, Pereira LM. Context-dependent incremental decision making scrutinizing the intentions of others via Bayesian network model construction. Intelligent Decision Technologies [Internet]. 2013:293–317.
Le Borgne Y, Bontempi G, Bonnechère B, Salvia P, Degelaen M, Van Sint Jan S. Data mining toolbox for gait analysis in children with cerebral palsy.
Traulsen A, Lenaerts T, Pacheco JM, Dingli D. On the dynamics of neutral mutations in a mathematical model for a homogeneous stem cell population. Journal of The Royal Society Interface [Internet]. 2013.
Lerat J-S, Han TA, Lenaerts T. Evolution of Common-pool Resources and Social Welfare in Structured Populations.
Lerat J-S, Han TA, Lenaerts T. Evolution of Common-Pool Resources and Social Welfare in Structured Populations.
Catteeuw D, Manderick B, Han TA. Evolutionary Stability of Honest Signaling in Finite Populations.
Lopes M, Bontempi G. Experimental assessment of static and dynamic algorithms for gene regulation inference from time series expression data. Frontiers in Genetics. 2013.
Le Borgne Y, Bonnechère B, Salvia P, Van Sint Jan S, Bontempi G. Fouille de données pour l’analyse de la marche de patients atteints d’infirmité motrice cérébrale (ICT4Rehab).
Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF. From protein sequence to dynamics and disorder with DynaMine. Nat Commun [Internet]. 2013.
Haibe-Kains B, Desmedt C, Di Leo A, Azambuja E, Larsimont D, Selleslags J, Delaloge S, Duhem C, Kains JP, Carly B, et al. Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients. Genomics Data. 2013.
Han TATAH, Pereira LM, Santos FC, Lenaerts T. Good agreements make good friends. Scientific reports [Internet]. 2013:2695.
Ben Taieb S, J Hyndman R. A gradient boosting approach to the Kaggle load forecasting competition. International Journal of Forecasting [Internet]. 2013:1–19.
Lerman L, Jr. JN, Veshchikov N. Improving Block Cipher Design by Rearranging Internal Operations. In: Samarati P SECRYPT 2013. SECRYPT 2013. ; 2013. p. 27-38.
Jansen M. Information criteria for variable selection under sparsity. {B}iometrika. 2013:–-.
Olsen C, Haibe-Kains B, Quackenbush J, Bontempi G. On the Integration of Prior Knowledge in the Inference of Regulatory Networks.
Han TA. Intention Recognition, Commitments and Their Roles in the Evolution of Cooperation: From Artificial Intelligence Techniques to Evolutionary Game Theory Models.; 2013 p. .
Han TA, Pereira LM. Intention-based Decision Making for Strategic Scenarios Dynamics via Computational Logic.
Guy Latouche, Mahmoodi S, Taylor PG. Level-phase independent stationary distributions for GI/M/1-type Markov chains with infinitely-many phases. Performance Evaluation. 2013:551–563.
Lerman L, Medeiros SF, Bontempi G, Markowitch O. A Machine Learning Approach Against a Masked AES. In: Francillon A, Rohatgi P CARDIS 2013. CARDIS 2013. ; 2013. p. 62–77.
Bontempi G, Ben Taieb S, Le Borgne Y. Machine Learning Strategies for Time Series Forecasting.
Bonnechere B, Wermenbol V, Dan B, Salvia P, Borgne Y-AL, Bontempi G, Vansummeren S, Sholukha V, Moiseev F, Jansen B, et al. Management and interpretation of medical data related to cerebral pasly: the ICT4 Rehab project. European journal of paediatric neurology. 2013:32.
Hautphenne S, Guy Latouche, Nguyen GT. Markovian trees subject to catastrophes: Would they survive forever?. In: Guy Latouche, Ramaswami V, Sethuraman J, Sigman K, Squillante MS, Yao DD Matrix-Analytic Methods in Stochastic Models. Vol. 27. Matrix-Analytic Methods in Stochastic Models. ; 2013. p. 87–106.
De Jay N, Papillon-Cavanagh S, Olsen C, El-Hachem N, Bontempi G, Haibe-Kains B. mRMRe: an R package for parallelized mRMR ensemble feature selection. Bioinformatics. 2013.
Jansen M. Multiscale local polynomial models for estimation and testing. In: Akritas M, Lahiri S N, Politis D Topics in NonParametric Statistics. Topics in NonParametric Statistics. ; 2013. p. To Appear.
Jansen M. Multiscale local polynomial smoothing in a lifted pyramid for non-equispaced data. IEEE Transactions on Signal Processing. 2013:545-555.
Jansen M. Noise reduction in an adaptive multiscale local polynomial decomposition.
Dendievel S, Guy Latouche, Liu Y. Poisson’s equation for discrete-time quasi-birth-and-death processes. Performance Evaluation. 2013:564–577.
Lerman L, Bontempi G, Markowitch O. Power analysis attack: an approach based on machine learning.International Journal of Applied Cryptography. 2013.
Dal Pozzolo A, Caelen O, Waterschoot S, Bontempi G. Racing for unbalanced methods selection.
Lerman L, Medeiros SF, Veshchikov N, Meuter C, Bontempi G, Markowitch O. Semi-Supervised Template Attack. In: Prouff E COSADE 2013. Vol. 7864. COSADE 2013. ; 2013. p. 184-199.
Govorun M, Guy Latouche, Remiche M-A. Stability for fluid queues: characteristic inequalities. Stochastic Models. 2013:64–88.
Moulos P, Kanaris I, Bontempi G. Stability of feature selection algorithms for classification in high-throughput genomics datasets.
Han TA, Pereira LM. State-of-the-Art of Intention Recognition and its Use in Decision Making – A Research Summary. AI Communication Journal (forthcoming) [Internet]. 2013.
Bontempi G. A statistic criterion for reducing indeterminacy in linear causal modeling. ICPRAM 2103 Conference. 2013.
Pini G, Gagliolo M, Brutschy A, Dorigo M, Birattari M. Task partitioning in a robot swarm: a study on the effect of communication. Swarm Intelligence. 2013:173–199.
Lerman L, Bontempi G, Ben Taieb S, Markowitch O. A Time Series Approach for Profiling Attack. In: Gierlichs B, Guilley S, Mukhopadhyay D Security, Privacy, and Applied Cryptography Engineering. Vol. 8204. Security, Privacy, and Applied Cryptography Engineering. ; 2013. p. 75-94.
Guy Latouche, Nguyen GT, Palmowski Z. Two-dimensional fluid queues with temporary assistance. In: Guy Latouche, Ramaswami V, Sethuraman

J, Sigman K, Squillante MS, Yao DD Matrix-Analytic Methods in Stochastic Models. Vol. 27. Matrix-Analytic Methods in Stochastic Models. ; 2013. p. 187–207.
Van Sint Jan S, Wermenbol V, Van Bogaert P, Desloovere K, Degelaen M, Dan B, Salvia P, Ortibus E, Bonnechere B, Borgne Y-AL, et al. Une plate-forme technologique liée à la paralysie cérébrale-Le projet ICT4Rehab. MS. Médecine sciences. 2013:7.
Han TA, Pereira LM, Santos FC, Lenaerts T. Why Is It So Hard to Say Sorry: The Evolution of Apology with Commitments in the Iterated Prisoner’s Dilemma.

Cilia E, Vuister GW, Lenaerts T. Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e. PLoS Comput Biol [Internet]. 2012:e1002794 – .
Vaccaro A, Bontempi G, Ben Taieb S, Villacci D. Adaptive local learning techniques for multiple-step-ahead wind speed forecasting. Electric Power Systems Research. 2012:129-135.
Youssef KK, Lapouge G, Bouvrée K, Rorive S, Brohée S, Appelstein O, Larsimont J-C, Sukumaran V, {Van de Sande} B, Pucci D, et al. Adult interfollicular tumour-initiating cells are reprogrammed into an embryonic hair follicle progenitor-like fate during basal cell carcinoma initiation. Nat
Cell Biol [Internet]. 2012:1282–1294.

Falda M, Toppo S, Pescarolo A, Lavezzo E, Di Camillo B, Facchinetti A, Cilia E, Velasco R, Fontana P. Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms. BMC Bioinformatics. 2012:S14.
Meyer PE, Bontempi G. Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data.

Jiang S, Guy Latouche, Liu Y. Computing issues for the steady probabilities for quasi-birth-death process with a continuous phase set based on wavelet transform.
Mihaylov {M, Le Borgne Y, Tuyls K, Nowé A. Decentralised reinforcement learning for energy-efficient scheduling in wireless sensor networks. International Journal of Communication Networks and Distributed Systems. 2012:207–224.
Mascré G, Dekoninck S, Drogat B, Youssef KK, Brohée S, Sotiropoulou PA, Simons BD, Blanpain C. Distinct contribution of stem and progenitor cells to epidermal maintenance. Nature [Internet]. 2012:257–262.
Brohée S, Bontempi G. D-peaks: A visual tool to display ChIP-seq peaks along the genome.Transcription. 2012.

van Segbroeck S, Pacheco JM, Lenaerts T, Santos FC. Emergence of Fairness in Repeated Group Interactions. Phys. Rev. Lett. [Internet]. 2012:158104.
Lopes M, Meyer P, Bontepi G. Estimation of temporal lags for the inference of gene regulatory networks from time series.

Hautphenne S, Guy Latouche, Nguyen GT. Extinction probabilities of branching processes with countably infinitely many types. Submitted for publication. 2012.
Borkar V, Ejov V, Filar JA, Nguyen GT. Hamiltonian cycles and Markov chains.; 2012 p. .
Krzesinski AE, Latouche G, Taylor PG. How do we encourage an egoist to act socially in an ad hoc mobile network?. Computer Networks. 2012:3499–3510.
Compté N, Pepersack T, Bontempi G, Goriely S. Innate cytokines production in the geriatric population: Frailty is associated with low responsiveness to lipopolysaccharide. European Geriatric Medicine. 2012:S75.
Lerman L, Markowitch O, Jr. NJ. Key Management as a Service.

Guy Latouche, Mahmoodi S, Taylor PG. Level-phase independent stationary distributions for GI/M/1-type Markov chains with infinitely-many phases. Submitted for publication. 2012.
Van Sint Jan S, Bontempi G, Summeren VS. Making the links between Rehabilitation and Musculoskeletal modelling: requirements and tools.

Hautphenne S, Guy Latouche. The Markovian binary tree applied to demography. J. Math. Biol. 2012:1109–1135.
Govorun M, Guy Latouche. Modeling the effect of health: Phase-type approach. Submitted for publication. 2012.
Jansen M. Multiscale local polynomial smoothing in a lifted pyramid for non-equispaced data. IEEE Transactions on Signal Processing. 2012.
Hautphenne S, Guy Latouche, Nguyen GT. On the nature of Phase-Type Poisson distributions. Submitted for publication. 2012.
Liu Y. Perturbation bounds for the stationary distributions of Markov chains. SIAM J. Matrix Anal. & Appl. 2012:1057–1074.
Dendievel S, Guy Latouche, Liu Y. Poisson’s equation for discrete-time quasi-birth-and-death processes. Submitted for publication. 2012.
Cilia E, Teso S, Ammendola S, Lenaerts T, Andrea P. Predicting virus mutations through relational learning. In: Annotation, Interpretation and Management of Mutations (AIMM) Workshop@ECCB2012. Vol. 916. Annotation, Interpretation and Management of Mutations (AIMM) Workshop@ECCB2012. ; 2012. p. .
Le Borgne Y, Bontempi G. Prediction-based data collection in wireless sensor networks.
Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M. Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks. Genome Research. 2012.
Govorun M, Guy Latouche, Remiche M-A. Profits and risks of pension plans. Performance Evaluation Review. 2012:41.
Huculeci R, Buts L, Lenaerts T, van Nuland NAJ, Garcia-Pino A. Purification, crystallization and preliminary X-ray diffraction analysis of the Fyn SH2 domain and its complex with a phosphotyrosine peptide. Acta Crystallographica Section F [Internet]. 2012:359–364.
Mihaylov {M, Le Borgne Y, Tuyls K, Nowé A. Reinforcement Learning for Self-Organizing Wake-Up Scheduling in Wireless Sensor Networks Filipe,
Joaquim; Fred A. Communications in Computer and Information Science. 2012:382-397.
Ben Taieb S, Bontempi G, Atiya A, Sorjamaa A. A review and comparison of strategies for multi-step ahead time series forecasting based on the NN5 forecasting competition. Expert systems with applications. 2012:7067–7083.
S. {Van Sint Jan}, B. {De Bono}, V. Sholukha, F. Moiseev, S. Vansummeren, Y. Le Borgne, G. Bontempi, B. Bonnechère, M. Rooze. SeedEP2 : Integrated Modelling of the Musculoskeletal System.
Van Sint Jan S, Bono DB, Sholukha V, Moiseev F, Vansummeren S, Le Borgne Y, Bontempi G, Bonnechère B, Rooze M. SeedEP2 : Integrated Modelling of the Musculoskeletal System.
`Dendievel S, Guy Latouche, Remiche M-A. Stationary distribution of a perturbed QBD process. Performance Evaluation Review. 2012:40.
Haibe-Kains B, Desmedt C, Loi S, Culhane AC, Bontempi G, Quackenbush J, Sotiriou C. A three-gene model to robustly identify breast cancer molecular subtypes. Journal of the National Cancer Institute. 2012:311–325.
Le Borgne Y, Bontempi G. Time series prediction for energy-efficient wireless sensors : Applications to environmental monitoring and video games.
Brohée S. Using the NeAT toolbox to compare networks to networks, clusters to clusters, and network to clusters. Methods Mol Biol [Internet]. 2012:327–342.

Huculeci R, Buts L, Lenaerts T, van Nuland NAJ. 1H, 13C and 15N backbone and side-chain chemical shift assignment of the Fyn SH2 domain and its complex with a phosphotyrosine peptide. Biomol NMR Assign [Internet]. 2011:181–4.
Vaccaro A, Bontempi G, Ben Taieb S, Villacci D. Adaptive local learning techniques for multiple-step-ahead wind speed forecasting. Electric Power Systems Research. 2011.
Mihaylov M, Le Borgne Y, Tuyls K, Nowé A. Distributed Cooperation in Wireless Sensor Networks.
Werner B, Dingli D, Lenaerts T, Pacheco JM, Traulsen A. Dynamics of Mutant Cells in Hierarchical Organized Tissues. PLoS Comput Biol [Internet]. 2011:e1002290.
Lenaerts T, Castagnetti F, Traulsen A, Pacheco JM, Rosti G, Dingli D. Explaining the in vitro and in vivo differences in leukemia therapy. Cell Cycle. 2011:1540–4.
Miranda A, Olsen C, Bontempi G. Fourier spectral factor model for prediction of multidimensional signals. Signal processing [Internet]. 2011.
Haibe-Kains B, Schroeder M, Culhane AC, Bontempi G, Sotiriou C, Quackenbush J. GeneFu: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer. [Internet]. 2011.
Desmedt C, A. DL, de Azambuja E, Larsimont D, B. H-K, J. S, Delaloge S, Duhem C, Kains JP, Carly B, et al.Multifactorial Approach to Predicting Resistance to Anthracyclines. Journal Clinical Oncology [Internet]. 2011.
Bontempi G, Haibe-Kains B, Desmedt C, Sotiriou C, Quackenbush J. Multiple-input multiple-output causal strategies for gene selection. BMC bioinformatics. 2011:458.
Bontempi G. An optimal stopping strategy for online calibration in local search.
Haibe-Kains B, Olsen C, Djebbari A, Bontempi G, Correll M, Bouton C, Quackenbush J. Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks. Nucleic Acids Research. 2011.
Caelen O, Cailloux O, Ghoundiwal D, Miranda AA, Barvais L, Bontempi G. Real-time prediction of an anesthetic monitor index using machine learning.
Ben Taieb S, Bontempi G. Recursive multi-step time series forecasting by perturbing data.
Cilia E, Landwehr N, Passerini A. Relational Feature Mining with Hierarchical Multitask kFOIL. Fundamenta Informaticae [Internet]. 2011:151–177.
Santos FC, Pinheiro FL, Lenaerts T, Pacheco JM. Role of diversity in the evolution of cooperation. Journal of theoretical biology [Internet]. 2011.
Bontempi G, Caelen O. A Selecting-the-Best Method for Budgeted Model Selection.
Segbroeck S, Santos F, Lenaerts T, Pacheco JM. Selection pressure transforms the nature of social dilemmas in adaptive networks. New Journal of Physics [Internet]. 2011.
Mihaylov M, Le Borgne Y, Tuyls K, Nowé A. Self-Organizing Synchronicity and Desynchronicity using Reinforcement Learning. Proceedings of the 3rd International Conference on Agents and Artificial Intelligence (ICAART 2011) [Internet]. 2011:94-103.
Lerman L, Bontempi G, Markowitch O. Side channel attack: an approach based on machine learning.

Haibe-Kains B, Schroeder M, Sotiriou C, Bontempi G, Quackenbush J. SurvComp: Performance Assessment and Comparison for Survival Analysis. [Internet]. 2011.

Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, et al.Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nature Medecine. 2010.
Cilia E, Passerini A. Automatic prediction of catalytic residues by modeling residue structural neighborhood. BMC bioinformatics [Internet]. 2010:115.

Bontempi G, Meyer PE. Causal filter selection in microarray data. ICML’10,

International Conference of Machine Learning [Internet]. 2010.
Segbroeck SV, Santos FC, Pacheco JM, Lenaerts T. Coevolution of Cooperation, Response to Adverse Social Ties and Network Structure. Games. 2010:317–337.
Iolis B, Bontempi G. Comparison of Selection Strategies in Monte Carlo Tree Search for Computer Poker. BeNeLearn2010, The annual machine learning conference of Belgium and The Netherlands. 2010.
Bontempi G, Ben Taieb S. Conditionally dependent strategies for multi-step-ahead prediction in local learning. International Journal of Forecasting. 2010.

Mihaylov M, Le Borgne Y, Nowé A, Tuyls K. Decentralized Reinforcement Learning for Wake-up Scheduling.
Le Borgne Y, Nowé A, Steenhaut K, Bontempi G. Demo Abstract: Demonstrating Principal Component Aggregation for Distributed Spatial Pattern Recognition. In: Abdelzaher T, Voigt T, Wolisz A Proceedings of the 9th IEEE/ACM Conference on Information Processing in Sensor Networks. Proceedings of the 9th IEEE/ACM Conference on Information Processing in Sensor Networks. ; 2010. p. 430-431.
Le Borgne Y, Nowé A, Steenhaut K. Distributed regression for high-level feature extraction in wireless sensor networks. In: Altman E, Basar T, Chlamtac I Proceedings of the 7th IEEE Conference on Networked Sensing Systems. Proceedings of the 7th IEEE Conference on Networked Sensing Systems. ; 2010. p. 249 – 252.
Caelen O, Bontempi G. A dynamic programming strategy to balance exploration and exploitation in the bandit problem. Annals of Mathematics and Artificial Intelligence. 2010.
Juul N, Eklund AC, Li Q, Burrell RA, Gerlinger M, Valero V, Andreopoulou E, Esteva FJ, Symmans FW, Desmedt C, et al. Evaluation of an RNA interference screen-derived mitotic and ceramide pathway meta- gene in paclitaxel-treated primary ER-/PR-/ERBB2- breast cancer: a retrospective analysis of five clinical trials. Lancet Oncology. 2010.
Dingli D, Traulsen A, Lenaerts T, Pacheco JM. Evolutionary dynamics of chronic myeloid leukemia. Genes Cancer [Internet]. 2010:309–15.
Cilia E, Passerini A. Frankenstein Junior: a relational learning approach toward protein engineering. Proceedings of the Annotation, Interpretation and Management of Mutations (AIMM) Workshop@ECCB2010 [Internet]. 2010.
Haibe-Kains B, Desmedt C, Rothé F, Piccart M, Sotiriou C, Bontempi G. A fuzzy gene expression-based computational approach improves breast cancer prognostication. Genome Biology. 2010.
Cilia E, Ammendola S. Identification of the amino acid residues affecting the catalytic pocket of the Sulfolobus solfataricus signature amidase. Protein and peptide letters [Internet]. 2010:146-50.
Segbroeck VS, Jong DS, Nowé A, Santos FC, Lenaerts T. Learning to coordinate in complex networks. Adaptive Behavoir [Internet]. 2010:416–427.
Abughalieh N, Le Borgne Y, Nowé A, Steenhaut K. Lifetime Optimization for Sensor Networks with Correlated Data Gathering. In: Altman E, Basar T, Chlamtac I Proceedings of the 7th IEEE Conference on Networked Sensing Systems. Proceedings of the 7th IEEE Conference on Networked Sensing Systems. ; 2010. p. 252 – 258.
Le Calvé B, Rynkowski M, Le Mercier M, Bruyère C, Lonez C, Gras T, Haibe-Kains B, Bontempi G, Decaestecker C, Ruysschaert JM, et al. Long term in vitro treatment of human glioblastoma cells with temozolomide increases resistance in vivo through up-regulation of GLUT transporter and aldo-keto reductase enzyme AKR1C expression. Neoplasia. 2010.
Lamoral-Theys D, Le Mercier M, Le Calvé B, Rynkowski MA, Bruyère C, Decaestecker C, Haibe-Kains B, Bontempi G, Dubois J, Lefranc F, et al. Long-term Temozolomide Treatment Induces Marked Amino Metabolism Modifications and an Increase in TMZ Sensitivity in Hs683 Oligodendroglioma Cells.Neoplasia. 2010.
Toussaint J, Durbecq V, Altintas S, Doriath V, Rouas G, Paesmans M, Bedard P, Haibe-Kains B, Tjalma WA, Larsimont D, et al. Low CD10 mRNA expression identifies high-risk ductal carcinoma in situ (DCIS). PLoS ONE. 2010.
Loi S, Haibe-Kains B, Majjaj S, Lallemand F, Durbecq V, Larsimont D, Gonzalez-Angulo AM, Pusztai L, Symmans FW, Bardelli A, et al. PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor positive breast cancer. PNAS. 2010.
Mascia F, Cilia E, Brunato M, Passerini A. Predicting Structural and Functional Sites in Proteins by Searching for Maximum-Weight Cliques. Proceedings of the Twenty-Fourth AAAI Conference on Artificial Intelligence (AAAI-10) [Internet]. 2010:1274–1279.
Haibe-Kains B, Culhane AC, Desmedt C, Bontempi G, Quackenbush J, Sotiriou C. Robustness of breast cancer molecular subtypes identification. Annals of Oncology. 2010.
Moore F, Naamane N, Colli ML, Bouckenooghe T, Ortis F, Gurzov EN, Igoillo-Esteve M, Mathieu C, Bontempi G, Thykjaer T, et al. STAT1 is a master regulator of pancreatic beta cells apoptosis and islet inflammation. J. Biol. Chem. 2010.
Dricot JM, Bontempi G, Doncker PD. Static and dynamic localization techniques for wireless sensor networks. In: Ferrari G Sensor Networks: Where Theory Meets Practice. Sensor Networks: Where Theory Meets Practice. ; 2010. p. .
Cilia E, Passerini A. Statistical and relational learning for understanding enzyme function. Dipartimento di Ingegneria e Scienza dell’Informazione, University of Trento [Internet]. 2010.
Lenaerts T, Pacheco JM, Traulsen A, Dingli D. Tyrosine kinase inhibitor therapy can cure chronic myeloid leukemia without hitting leukemic stem cells. Haematologica. 2010:900–7.

Loi S, Haibe-Kains B, Lallemand F, Pusztai L, Bardelli A, Gillett C, Ellis P, Piccart-Gebhart MJ, Phillips WA, McArthur GA, et al. Correlation of PIK3CA mutation-associated gene expression signature (PIK3CA-GS) with deactivation of the PI3K pathway and with prognosis within the luminal-B ER+ breast cancers. J Clin Oncol (Meeting Abstracts). 2009:533-.
Lenaerts T, Defaweux A, van Hemert J. The Evolutionary Transition Algorithm: Evolving Complex Solutions Out of Simpler Ones. Nature-Inspired Algorithms for Optimisation [Internet]. 2009:103–131.
Le Mercier M, Fortin S, Mathieu V, Roland I, Spiegl-Kreinecker S, Haibe-Kains B, Bontempi G, Decaestecker C, Berger W, Lefranc F, et al. Galectin 1 proangiogenic and promigratory effects in the Hs683 oligodendroglioma model are partly mediated through the control of BEX2 expression. Neoplasia. 2009:485–496.
Kontos K. Gaussian Graphical Model Selection for Gene Regulatory Network Reverse Engineering and Function Prediction.

Kontos K, André B, van Helden J, Bontempi G. Gaussian Graphical Models to Infer Putative Genes Involved in Nitrogen Catabolite Repression in \textitS. cerevisiae. In: Pizzuti C, Ritchie MD, Giacobini MProceedings of the 7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2009). Vol. 5483. Proceedings of the 7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2009). ; 2009. p. 13-24.
Desmedt C, Giobbie-Hurder A, Neven P, Paridaens R, Christiaens MR, Smeets A, Lallemand F, Haibe-Kains B, Viale G, Gelber R, et al. The Gene expression Grade Index: a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1-98 trial. BMC Medical Genomics. 2009:40.
Stamatopoulos B, Haibe-Kains B, Equeter C, Meuleman N, Soree A, De Bruyn C, Hanosset D, Bron D, Martiat P, Lagneaux L, et al. Gene expression profiling reveals differences in microenvironment interaction between patients with chronic lymphocytic leukemia expressing high versus low ZAP70 mRNA. Haematologica. 2009:790-799.
Liedtke C, Hatzis C, Symmans WF, Desmedt C, Haibe-Kains B, Valero V, Kuerer H, Hortobagyi GN, Piccart-Gebhart M, Sotiriou C, et al. Genomic Grade Index Is Associated With Response to Chemotherapy in Patients With Breast Cancer. J Clin Oncol. 2009:3185-3191.
Haibe-Kains B. Identification and Assessment of Gene Signatures in Human Breast Cancer.
Kontos K, Bontempi G. An Improved Shrinkage Estimator to Infer Regulatory Networks with Gaussian Graphical Models.
Toussaint J, Sieuwerts A, Haibe-Kains B, Desmedt C, Rouas G, Harris A, Larsimont D, Piccart M, Foekens J, Durbecq V, et al. Improvement of the clinical applicability of the Genomic Grade Index through a qRT-PCR test performed on frozen and formalin-fixed paraffin-embedded tissues. BMC Genomics. 2009:424.
Lenaerts T, Ferkinghoff-Borg J, Schymkowitz JWH, Rousseau F. Information theoretical quantification of cooperativity in signalling complexes. BMC Systems Biology [Internet]. 2009:9.
Le Borgne Y. Learning in Wireless Sensor Networks for Energy-Efficient Environmental Monitoring.
Stamatopoulos B, Meuleman N, Haibe-Kains B, Saussoy P, Van Den Neste E, Michaux L, Heimann P, Martiat P, Bron D, Lagneaux L, et al. microRNA-29c and microRNA-223 down-regulation has in vivo significance in chronic lymphocytic leukemia and improves disease risk stratification. Blood. 2009:5237-5245.
Cilia E, Landwehr N, Passerini A. Mining Drug Resistance Relational Features with Hierarchical Multitask kFOIL. Proceedings of BioLogical@AI*IA2009 [Internet]. 2009.

Ravoet M, Sibille C, Gu C, Libin M, Haibe-Kains B, Sotiriou C, Goldman M, Roufosse F, Willard-Gallo K. Molecular profiling of CD3-CD4+ T cells from patients with the lymphocytic variant of hypereosinophilic syndrome reveals targeting of growth control pathways. Blood. 2009:blood-2008-08-175091.
Lenaerts T, Schymkowitz JWH, Rousseau F. Protein domains as information processing units. Curr Protein Pept Sci. 2009:133–45.
Vanhee P, Stricher F, Baeten L, Verschueren E, Lenaerts T, Serrano L, Rousseau F, Schymkowitz JWH. Protein-peptide interactions adopt the same structural motifs as monomeric protein folds. Structure [Internet]. 2009:1128–36.
Segbroeck VS, Santos FC, Lenaerts T, Pacheco JM. Reacting differently to adverse ties promotes cooperation in social networks. Phys Rev Lett. 2009:058105.
Caelen O. {Sélection Séquentielle en Environnement Aléatoire Appliquée à l’Apprentissage Supervisé.
Lenaerts T, Defaweux A. Solving hierarchically decomposable problems with the Evolutionary Transition Algorithm. Natural intelligence for scheduling, planning and packing problems [Internet]. 2009:111–143.
Segbroeck SV, Nowé A, Lenaerts T. Stochastic simulation of the chemoton. Artif Life. 2009:213–26.
Lefranc F, Spiegl-Kreinecker S, Haibe-Kains B, Bontempi G, Decaestecker C, Berger W, Kiss R. Temozolomide displays antimigratory effects in human glioblastoma cells mediated through neuregulin-1 down-regulation. Surgical Neurology. 2009:134 – 134.
Bontempi G, Caelen O, Goffaux C. On the use of supervised learning techniques to speed up the design of aeronautics components.

Bontempi G. Bandwidth selection for multiple-step-ahead time series prediction: beyond cross-validation.
Desmedt C, Haibe-Kains B, Wirapati P, Buyse M, Larsimont D, Bontempi G, Delorenzi M, Piccart M, Sotiriou C. Biological Processes Associated with Breast Cancer Clinical Outcome Depend on the Molecular Subtypes. Clin Cancer Res [Internet]. 2008:5158-5165.
Stamatopoulos B, Haibe-Kains B, Meuleman N, Bron D, Martiat P, Lagneaux L. CLL patient comparison according to Zap70 mRNA level: new prognostic factors, differences in microRNA expression and distinct interaction capacities with the microenvironment.
Haibe-Kains B, Desmedt C, Sotiriou C, Bontempi G. A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?. Bioinformatics [Internet]. 2008:2200-2208.
Haibe-Kains B, Desmedt C, Piette F, Buyse M, Cardoso F, van’t Veer L, Piccart M, Bontempi G, Sotiriou C. Comparison of prognostic gene expression signatures for breast cancer. BMC Genomics [Internet]. 2008:394.
Haibe-Kains B, Desmedt C, Loi S, Delorenzi M, Sotiriou C, Bontempi G. Computational Intelligence in Clinical Oncology : Lessons Learned from an Analysis of a Clinical Study. In: Applications of Computational Intelligence in Biology. Vol. 122. Applications of Computational Intelligence in Biology. ; 2008. p. 237-268.
Sotiriou C, C.Equeter, Ouriaghli EF, Haibe-Kains B, Durbecq V, Larsimont D, Igniatiadis M, Desmedt C, Willard-Gallo K, Piccart MJ, et al. Correlation of gene expression analysis of tumor-infiltrating CD4+ cells with immune function and survival according to different breast cancer (BC) molecular subtypes. In: of Oncology JC ASCO Annual Meeting Proceedings. Vol. 20. ASCO Annual Meeting Proceedings. ; 2008. p. .
Bontempi G, Vaccaro A, Villacci D. Data driven calibration of Power Conductors Thermal Model for Overhead Lines overload protection. International Journal of Reliability and Safety. 2008:5-18.

Le Borgne Y, S. Raybaud, Bontempi G. Distributed principal component analysis for wireless sensor networks. Sensors Journal [Internet]. 2008:4821–4850.
Le Borgne Y, Raybaud S, Bontempi G. Distributed principal component analysis for wireless sensor networks. Sensors Journal. 2008:4821–4850.

Gershenson C, Lenaerts T. Evolution of complexity. Artif Life [Internet]. 2008:241–3.
Segbroeck SV, Santos FC, Nowé A, Pacheco JM, Lenaerts T. The evolution of prompt reaction to adverse ties. BMC Evol Biol [Internet]. 2008:287.

Caelen O, Bontempi G. On the evolution of the expected gain of a greedy action in the bandit problem.
Journe F, Durbecq V, Haibe-Kains B, Chaboteaux C, Rouas G, Laurent G, Larsimont D, Piccart MJ, Body JJ, Sotiriou C, et al. Farnesoid X receptor (FXR) status complements the evaluation of estrogen receptor alpha (ER) in breast cancer (BC) patients and predicts benefit from tamoxifen. European Journal of Cancer Supplements. 2008:112.
Stamatopoulos B, Haibe-Kains B, Meuleman N, Bron D, Martiat P, Lagneaux L. Gene expression profiles based on ZAP70 mRNA level.

Olsen C, Meyer PE, Bontempi G. On the impact of entropy estimator in transcriptional regulatory network inference.
Meyer PE, Schretter C, Bontempi G. Information-Theoretic Feature Selection in Microarray Data using Variable Complementarity. IEEE Journal of Selected Topics in Signal Processing. 2008:261-274.
Le Mercier M, Mathieu V, Haibe-Kains B, Bontempi G, Mijatovic T, Decaestecker C, Kiss R, Lefranc F. Knocking Down Galectin 1 in Human Hs683 Glioblastoma Cells Impairs Both Angiogenesis and Endoplasmic Reticulum Stress Responses. Journal of Neuropathology and Experimental Neurology. 2008:356-469.
Bontempi G. Long Term Time Series Prediction with Multi-Input Multi-Output Local Learning.
Kontos K, Godard P, André B, van Helden J, Bontempi G. Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast \textitSaccharomyces cerevisiae. BMC Proceedings. 2008:S5.
Wirapati P, Sotiriou C, Kunkel S, Farmer P, Pradervand S, Haibe-Kains B, Desmedt C, Ignatiadis M, Sengstag T, Schutz F, et al. Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Research [Internet]. 2008:R65.
Sotiriou C, Loi S, McArthur G, Haibe-Kains B. Method and kit for the detection of genes associated with PIK3CA mutation and involved in PI3K/AKT pathway activation in the ER-positive and HER2- positive subtypes with clinical implications. [Internet]. 2008.
Sotiriou C, Desmedt C, Haibe-Kains B. Methods and tools for prognosis of cancer in ER- patients. [Internet]. 2008.
Sotiriou C, Desmedt C, Haibe-Kains B. Methods and tools for prognosis of cancer in HER2+ patients. [Internet]. 2008.
Meyer PE, Lafitte F, Bontempi G. MINET: An open source R/Bioconductor Package for Mutual Information based Network Inference. BMC Bioinformatics. 2008.
Bontempi G, Meyer PE. A model-based relevance estimation approach for feature selection in microarray datasets. In: Proceedings of ICANN 2008. Vol. II. Proceedings of ICANN 2008. ; 2008. p. 21-31.
Dricot JM, Van Der Haegen M, Le Borgne Y, Bontempi G. A Modular Framework for User Localization and Tracking Using Machine Learning Techniques in Wireless Sensor Networks
Dricot JM, Van Der Haegen M, Le Borgne Y, Bontempi G. A Modular Framework for User Localization and Tracking Using Machine Learning Techniques in Wireless Sensor Networks.
Toussaint J, Sieuwerts A, Durbecq V, Haibe-Kains B, Berns E, Harris AL, Larsimont D, Piccart M, Foekens J, Sotiriou C, et al. Molecular qRT-PCR grade index: a new tool for breast cancer (BC) patient grading improvement. European Journal of Cancer Supplements. 2008:140.
Kontos K, Bontempi G. Nested $q$-Partial Graphs for Genetic Network Inference from “Small $n$, Large $p$” Microarray Data.
Kontos K, Bontempi G. Nested $q$-Partial Graphs for Genetic Network Inference from “Small $n$, Large $p$” Microarray Data. In: Elloumi M, Küng J, Linial M, Murphy R, Schneider K, Toma C Proceedings of the 2nd International Conference on Bioinformatics Research and Development (BIRD 2008). Proceedings of the 2nd International Conference on Bioinformatics Research and Development (BIRD 2008). ; 2008. p. 273-287.
Miranda AA, Le Borgne Y, Bontempi G. New Routes from Minimal Approximation Error to Principal Components. Neural Processing Letters, Springer Netherlands. 2008:197 – 207.
Miranda {AA }, Le Borgne Y, Bontempi G. New Routes from Minimal Approximation Error to Principal Components. Neural Processing Letters. 2008:197 – 207.
Mijatovic T, Neve DN, Gailly P, Mathieu V, Haibe-Kains B, Bontempi G, Lapeira J, Decaestecker C, Facchini V, Kiss R, et al. Nucleolus and c-Myc: potential targets of cardenolide-mediated antitumor activity. Mol Cancer Ther [Internet]. 2008:1285-1296.
Journe F, Durbecq V, Chaboteaux C, Rouas G, Haibe-Kains B, IdBoufker H, Laurent G, Sotiriou C, Larsimont D, Body JJ, et al. OC3. Farnesoid X receptor (FXR): A new marker for the prediction of bone metastases in breast cancer. Cancer treatment reviews [Internet]. 2008:50.
Dricot JM, Van Der Haegen M, Le Borgne Y, Bontempi G. Performance Evaluation of Machine Learning Technique for the Localization of Users in Wireless Sensor Networks. In: Wehenkel L, Geurts P, Marée RProceedings of the BENELEARN Machine Learning Conference. Proceedings of the BENELEARN Machine Learning Conference. ; 2008. p. 93-94.
Loi S, Haibe-Kains B, Desmedt C, Wirapati P, Lallemand F, Tutt A, Gillet C, Ellis P, Ryder K, Reid J, et al.Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics [Internet]. 2008:239.
Le Borgne Y, Dricot JM, Bontempi G. Principal Component Aggregation for Energy-efficient Information Extraction in Wireless Sensor Networks.
Le Borgne Y, Dricot JM, Bontempi G. Principal Component Aggregation for Energy-efficient Information Extraction in Wireless Sensor Networks.
Lenaerts T, Ferkinghoff-Borg J, Stricher F, Serrano L, Schymkowitz JWH, Rousseau F. Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure. BMC Struct Biol [Internet]. 2008:43.
Baeten L, Reumers J, Tur V, c}ois Stricher F{\c, Lenaerts T, Serrano L, Rousseau F, Schymkowitz JWH. Reconstruction of protein backbones from the BriX collection of canonical protein fragments. PLoS Computational Biology [Internet]. 2008:e1000083.
Lenaerts T, Bersini H. A Synthon Approach to Artificial Chemistry. Artif Life [Internet]. 2008.
Mijatovic T, Mahieu T, De Neve N, Dewelle J, Simon G, Dehoux MJM, van der Aar E, Haibe-Kains B, Bontempi G, Deacestecker C, et al. UNBS5162, a Novel Naphthalimide That Decreases CXCL Chemokine Expression in Experimental Prostate Cancers. Neoplasia. 2008:573-586.
Le Mercier M, Lefranc F, nd Debeir MTO, Haibe-Kains B, Bontempi G, Decaestecker C, Kiss R, Mathieu V. vidence of galectin-1 involvement in glioma chemoresistance. Toxicology and Applied Pharmacology. 2008:172-183.

Megalizzi V, Mathieu V, Mijatovic T, Gailly P, Debeir O, Neve DN, Damme VM, Bontempi G, Haibe-Kains B, Decaestecker C, et al. 4-IBP, a sigma(1) Receptor Agonist, Decreases the Migration of Human Cancer Cells, Including Glioblastoma Cells, In Vitro and Sensitizes Them In Vitro and In Vivo to Cytotoxic Insults of Proapoptotic and Proautophagic Drugs. Neoplasia. 2007:358-369.
Le Borgne Y, Santini S, Bontempi G. Adaptive Model Selection for Time Series Prediction in Wireless Sensor Networks. Journal of Signal Processing. 2007:3010-3020.
Cilia E, Moschitti A. Advanced Tree-Based Kernels for Protein Classification. Proceedings of AI*IA 2007 [Internet]. 2007:218-229.
Sotiriou C, Desmedt C, Haibe-Kains B, Harris A, Larsimont D, Buyse M, Wirapati P, Delorenzi M, Bontempi G, Piccart MJ, et al. Biological mechanisms that trigger breast cancer (BC) tumor progresion are molecular subtype dependent.
Bontempi G. A blocking strategy to improve gene selection for classification of gene expression data.IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2007:293-300.
Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt A, Gillett C, Harris A, Bergh J, Foekens J, Klijn J, et al.Definition of clinically distinct molecular subtypes in estrogen receptor positive breast carcinomas through use of genomic grade. Journal of Clinical Oncology. 2007.
Godard {P, Urrestarazu A, Vissers S, Kontos K, Bontempi G, van Helden J, André B. Effect of 21 Different Nitrogen Sources on Global Gene Expression in the Yeast \textitSaccharomyces cerevisiae. Molecular and Cellular Biology. 2007:3065-3086.
Pacheco JM, Lenaerts T, Santos F. Evolution of Cooperation in a Population of Selfish Adaptive Agents. LECTURE NOTES IN COMPUTER SCIENCE [Internet]. 2007.
Loi S, Haibe-Kains B, Desmedt C, Sotiriou C. Expression Profiling in Breast Carcinoma: New Insights on Old Prognostic Factors?. Journal of Clinical Oncology. 2007:4317-4318.
Samatopoulos B, Equeter C, Haibe-Kains B, Soree A, Sotiriou C, Bron D, Martiat P, Lagneaux L. Gene expression comparison between B cells expressing high and low level of Zap-70 mRNA reveals distinct profiles, potential therapeutic targets and new prognostic factors for Chronic Lymphocytic Leukemia.
Caelen O, Bontempi G. Improving the exploration strategy in bandit algorithms. In: in Science LNCProceedings of Learning and Intelligent OptimizatioN LION II. Proceedings of Learning and Intelligent OptimizatioN LION II. ; 2007. p. 56-68.
Le Borgne Y, Van Der Haegen M, Bontempi G. Localization for Wireless Sensor Networks with CC2420 Radios. In: Proceedings of the 7th international conference on new technologies of distributed systems. Vol. 1. Proceedings of the 7th international conference on new technologies of distributed systems. ; 2007. p. 23-28.
Caelen O, Bontempi G, Barvais L. Machine learning techniques for decision support tool in anesthesia.
Kontos K, Godard P, André B, van Helden J, Bontempi G. Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast \textitSaccharomyces cerevisiae.
Meyer PE, F.Lafitte, G.Bontempi. minet: Mutual Information NETwork inference. [Internet]. 2007.
Santos F, Bersiniłdots} H, Lenaerts T. Networks regulating networks: the effects of constraints on topological evolution. Proceedings of the 9th European conference in Advances in Artificial Life [Internet]. 2007:956–965.
Loi S, Sotiriou C, Haibe-Kains B, Lallemand F, Conus N, Piccart MJ, Speed T, McArthur GA. Overcoming tamoxifen resistance in the luminal B subtype by targeting activated HER2 (ERBB2) signaling in the absence of HER2 overexpression: tailoring treatment in hormone responsive breast cancer.
Norguet JP, Tshibasu-Kabeya B, Bontempi G, Zimanyi E. A Page-Classification Approach to Web Usage Semantic Analysis. Engineering Letters, Special Issue: Soft computing in Artificial Intelligence, Data and Web Mining, Machine Learning (Part I). 2007.
Desmedt C, Piette F, Loi S, Wang Y, Lallemand F, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, Saghatchian d’Assignies M, et al. Strong time-dependency of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multi-centre independent validation series. Clinical Cancer Research. 2007:3207-14.
Desmedt C, Piette F, Cardoso F, Wang Y, Loi S, Lallemand F, Klijn J, Haibe-Kains B, Viale G, Delorenzi M, et al. TRANSBIG multi-centre independent validation of the Rotterdam 76-gene prognostic signature for patients with node-negative breast cancer.
Durbecq V, Toussaint J, Haibe-Kains B, Desmedt C, Rouas G, Larsimont D, Buyse M, Bontempi G, Piccart MJ, Sotiriou C, et al. Transforming genomic grade index (GGI) into a user-friendly qRT-PCR tool which will assist clinicians and patients in optimizing treatment of early breast cancer (BC).
Le Borgne Y, Bontempi G. Unsupervised and Supervised Compression with Principal Component Analysis in Wireless Sensor Networks.
Stamatopoulos B, Heuleman N, Haibe-Kains B, Duvillier H, Massy M, Martiat P, Bron D, Lagneaux L. Zap-70 mRNA expression quantified in B cell by real time PCR is a powerful prognostic factor in Chronic Lymphocytic Leukemia.

Villacci D, Bontempi G, Vaccaro A. An adaptive local learning based methodology for voltage regulation in distribution networks with dispersed generation. IEEE Transactions on Power Systems. 2006:1131-1140.
Tshibasu-Kabeya B, Bontempi G, Beaugendre F, Marechal G. AIDAR: Une architecture pour l’indexation de documents audionumériques.
Equeter C, Ouriaghli EF, Haibe-Kains B, Stamatopoulos B, André F, Lallemand F, Filippov V, Larsimont D, Sotiriou C, Willard-Gallo K, et al. CD4+ T cells infiltrating breast tumors exhibit altered expression of T cell immune response genes in comparison with their counterparts from the lymph node and blood.
Haibe-Kains B, Sotiriou C, Bontempi G. Class Discovery and Class Prediction from Human Cancer Microarray Datasets.
Sotiriou C, Wirapati P, Loi S, Haibe-Kains B, Desmedt C, Tutt A, Ellis P, Buyse M, Delorenzi M, Piccart M, et al. Comprehensive analysis integrating both clinicopathological and gene expression data in more than 1500 samples: Proliferation captured by gene expression grade index appears to be the strongest prognostic factor in breast cancer (BC).
Sotiriou C, Haibe-Kains B, Desmedt C, Wirapati P, Durbecq V, Harris A, Larsimont D, Bontempi G, Buyse M, Delorenzi M, et al. Comprehensive molecular analysis of several prognostic signatures using molecular indices related to hallmarks of breast cancer: proliferation index appears to be the most significant component of all signatures.
Santos FC, Pacheco JM, Lenaerts T. Cooperation prevails when individuals adjust their social ties. PLoS Comput Biol. 2006:e140.
Santos FC, Pacheco JM, Lenaerts T. Evolutionary dynamics of social dilemmas in structured heterogeneous populations. Proc Natl Acad Sci USA [Internet]. 2006:3490–4.
Desmedt C, Azambuja E, Di Leo A, Larsimont D, Durbecq V, Antoine D, Lallemand F, Haibe-Kains B, Cardoso F, Nogaret JM, et al. Gene expression profiling can predict pathological complete response (pCR) to anthracycline-monotherapy in estrogen-receptor (ER) negative breast cancer
(BC) patients.
Sotiriou C, Wirapati P, Loi SM, Desmedt C, Durbecq V, Harris A, Bergh J, Smeds J, Haibe-Kains B, Larsimont D, et al. Gene expression profiling in breast cancer: Understanding the molecular basis of histologic grade to improve prognosis. Journal of National Cancer Institute. 2006:262-272.
Sotiriou C, Wirapati P, Loi S, Haibe-Kains B, Piette F, Buyse M, Bontempi G, Delorenzi M, Piccart M. Is genomic grading killing histological grading ?. In: Journal of European Breast Cancer. Vol. 4. Journal of European Breast Cancer. ; 2006. p. 177.
Bersini H, Lenaerts T, Santos FC. Growing biological networks: beyond the gene-duplication model. Journal of Theoretical Biology [Internet]. 2006:488–505.
Caelen O, Bontempi G, Coussaert E, Barvais L, Clement F. Machine Learning Techniques to Enable Closed-Loop Control in Anesthesia.
Caelen O, Engelman E, Schmartz D, Bontempi G, Barvais L. Preliminary Results of Data Mining in BIS guided Propofol-Remifentanil TCI Anaesthesia(abstract).
Bejjani G, Caelen O, Bontempi G, Perrin L, Barvais L. Retrospective comparison of manual versus semi-automated propofol-remifentanil TCI Anaesthesia (abstract).
Kontos K, Bontempi G. Scale-free paradigm in yeast genetic regulatory network inferred from microarray data. In: Kovacs T, Marshall JAR Proceedings of AISB’06: Adaptation in Artificial and Biological Systems. Vol. 3. Proceedings of AISB’06: Adaptation in Artificial and Biological Systems. ; 2006. p. 139-144.
Le Borgne Y, Moussaid M, Bontempi G. Simulation Architecture for Data Processing Algorithms in Wireless Sensor Networks.
Caelen O, Bontempi G, Clement F, Coussaert E, Barvais L. Simulation assessment of a closed-loop controller designed by machine learning techniques(abstract).
Cilia E, Moschitti A, Ammendola S, Basili R. Structured Kernels for the Automatic Detection of Protein Active Sites. Proceedings of Mining and Learning with Graphs@ECML/PDKK [Internet]. 2006.

Bontempi G, Le Borgne Y. An Adaptive Modular Approach to the Mining of Sensor Network Data.
Bontempi G, Le Borgne Y. An Adaptive Modular Approach to the Mining of Sensor Network Data.
Sotiriou C, Wirapati P, Loi S, Desmedt C, Durbecq V, Harris A, Bergh J, Smeds J, Haibe-Kains B, Larsimont D, et al. Better characterization of estrogen receptor (ER) positive luminal subtypes using genomic grade. In: Breast Cancer Research and Treatment. Vol. 94. Breast Cancer Research and Treatment. ; 2005. p. S19.
Le Borgne Y. Bias-variance Trade-Off Characterization in a Classification Problem. What Differences with Regression?.
Sotiriou C, Wirapati P, Loi SM, Desmedt C, Durbecq V, Harris A, Bergh J, Smeds J, Haibe-Kains B, Larsimont D, et al. Breast tumours with intermediate histological grade can be reclassified into prognostically distinct groups by gene expression profiling. In: Breast Cancer Research and Treatment. Vol. 94. Breast Cancer Research and Treatment. ; 2005. p. S30.
Bontempi G, Birattari M, Meyer PE. Combining Lazy Learning, Racing and Subsampling for Effective Feature Selection.
Chu D, Lee H-C, Lenaerts T. Evolution of DNA uptake signal sequences. Artif Life [Internet]. 2005:317–38.
Lenaerts T, Jansen B, Tuyls K, Vylder BD. The evolutionary language game: an orthogonal approach. Journal of Theoretical Biology [Internet]. 2005:566–82.
Desmedt C, Loi SM, Haibe-Kains B, Soree A, Lallemand F, Durbecq V, Larsimont D, Tutt A, Ellis P, Gillett C, et al. Four genes by RT-PCR predicts distant relapse for women given adjuvant tamoxifen. In: Breast Cancer Research and Treatment. Vol. 94. Breast Cancer Research and Treatment. ; 2005. p. S129.
Bontempi G, Birattari M. From Linearization to Lazy Learning: A Survey of Divide-and-Conquer Techniques for Nonlinear Control. International Journal of Computational Cognition. 2005:56-73.
Sotiriou C, Wirapati P, Loi S, Harris A, Bergh J, Smeds J, Farmer P, Praz V, Haibe-Kains B, Lallemand F, et al. Gene Expression Profiling in Breast Cancer Challenges the Existence of Intermediate Histological Grade.
Caelen O, Bontempi G. How to allocate a restricted budget of leave-one-out assessments for effective model selection in machine learning: a comparison of state-of-the-art techniques.
Loi S, Desmedt C, Haibe-Kains B, Lallemand F, Gillett C, Tutt A, Ryder K, Ellis P, Harris A, Smeds J, et al.Predicting relapse in estrogen receptor (ER) positive breast cancer (luminal) subgroups treated with adjuvant tamoxifen. In: Breast Cancer Research and Treatment. Vol. 94. Breast Cancer Research and Treatment. ; 2005. p. S129.
Loi S, Piccart M, Haibe-Kains B, Desmedt C, A.Harris, Bergh J, Ellis P, Miller L, Liu E, Sotiriou C, et al.Prediction of early distant relapses on tamoxifen in early- stage breast cancer (BC): a potential tool for adjuvant aromatase inhibitor (AI) tailoring.
Villacci D, Bontempi G, Vaccaro A, Birattari M. The role of learning methods in the dynamic assessment of power components loading capability. IEEETransactions on Industrial Electronics. 2005.
Le Borgne Y, Bontempi G. Round Robin Cycle for Predictions in Wireless Sensor Networks. In: Palaniswami M Proceedings of the 2nd International Conference on Intelligent Sensors, Sensor Networks and Information Processing (ISSNIP). Proceedings of the 2nd International Conference on Intelligent Sensors, Sensor Networks and Information Processing (ISSNIP). ; 2005. p. 253-258.
Cilia E, Fabbri A, Uriani M, Scialdone GG, Ammendola S. The signature amidase from Sulfolobus solfataricus belongs to the CX3C subgroup of enzymes cleaving both amides and nitriles. Ser195 and Cys145 are predicted to be the active site nucleophiles. The FEBS journal [Internet]. 2005:4716-24.
Bontempi G. Structural feature selection for wrapper methods.

Lacroix M, Haibe-Kains B, Laes JF, Hennuy B, Lallemand F, Gonze I, Cardoso F, Piccart M, Leclercq G, Sotiriou C, et al. Gene Regulation by Phorbol 12-myristate 13-acetate (PMA) in two Jighly Different Breast Cancer Cell Lines. Oncology Report. 2004.
Bontempi G, Vaccaro A, Villacci D. Power cables thermal protection by interval simulation of imprecise dynamical systems. IEE Proceedings of Generation Transmission and Distribution. 2004.
Bontempi G, Vaccaro A, Villacci D. A semi-physical modelling architecture for dynamic assessment of power components loading capability. IEE Proceedings of Generation Transmission and Distribution. 2004:533-542.
Bontempi G, Kruijtzer W. The use of intelligent data analysis techniques for system-level design: a software estimation example. Soft Computing Journal. 2004:477-490.

Bontempi G, Bersini H, Birattari M. The local paradigm for modeling and control: From neuro-fuzzy to lazy learning. Fuzzy Sets and Systems. 2001:59-72.

Bontempi G, Birattari M, Bersini H. Lazy learning for modeling and control design. International Journal of Control. 1999:643-658.

Anon.

Bini DA, Dendievel S, Guy Latouche, Meini B. Computing the exponential of large block-triangular block-Toeplitz matrices encountered in fluid queues.
Hautphenne S, Guy Latouche, Nguyen GT. Extinction probabilities of branching processes with countably infinitely many types.
Guy Latouche, Nguyen GT. Fluid approach to two-sided Markov-modulated Brownian motion.
Lerman L, Medeiros SF, Bontempi G, Markowitch O. A Machine Learning Approach Against a Masked AES. In: Francillon A, Rohatgi P Smart Card Research and Advanced Applications. Smart Card Research and Advanced Applications. ; p. 61-75.
Guy Latouche, Nguyen GT. The morphing of fluid queues into Markov-modulated Brownian motion.
De Jay N, Papillon-Cavanagh S, Olsen C, Bontempi G, Haibe-Kains B. mRMRe: an R package for parallelized mRMR ensemble feature selection.
Hautphenne S, Guy Latouche, Nguyen GT. On the nature of Phase-Type Poisson distributions.
Guy Latouche, Miyazawa M. Product-form characterization for a two-dimensional reflecting random walk.
Ben Taieb S, J Hyndman R. Recursive and direct multi-step forecasting : the best of both worlds.
Govorun M, Guy Latouche, Remiche M-A. Stability for fluid queues: characteristic inequalities.
Jiang S, Guy Latouche, Liu Y. Wavelet transforms for quasi-birth-and-death processes with a continuous phase set.